It Started Like This
by Sean Son of Athena
Summary: When Ashley and Vega's Daughter has to stay at Shepard's house while they're away on a mission what will happen if the Vega's don't return from their mission
1. Chapter 1

_**Just a little back story, it follows about a year after Kelly's hero ends, if you haven't read it i recommend you do, and I apologize for its slow beginning but it gets a lot better after a few chapters.**_

Kelly opened the door with a cheerfully smile. Bailey was standing there next to her father James Vega, she was holding a luggage bag that contained a few days of clothing. "Welcome Bailey here let me take your bags" said Kelly as she held out her hand.

"Thanks mrs. Shepard, I hope I'm not to much trouble" answered Bailey as she passed her bag to Kelly.

"Bailey can you go inside please, I want to speak to your father for a moment" said Kelly as Shepard appeared next to her.

"Sure" then she turned around and hugged her father and went inside the house.

"So can you tell us where you two are going?" Asked Kelly as she checked to make sure that Kaiden and Bailey weren't listening. "Is the council sending you two back to Omega?"

"No... I mean I can't tell you, its some top secret mission that she won't tell me completely about... all i know is that it is extremely important."

Shepard knew all about the mission. He was still registered as a Spectre but had "retired" from duty. He had read the mission briefing before Ashley had given James the "edited version of the dossier. From what he had read they were going to check on the situations with the Leviathan race that Shepard had recruted prior to the assault on earth.

"Okay well, be careful... wherever you're going" winked Shepard. "If you need back up, make sure to call... and I'm sure I can get a few of our old friends to come help out also." Promised the former commander. James quickly shook his hand and turned around to return to his car.

Kelly shut the door after a few moments. "Thats weird, why wasn't Ashley here to say bye to her daughter?" She asked. "You don't think she's still mad about my physiological report, do you?"

"I hope not" prayed Shepard, "they should be back next week." Then Kelly grabbed hold of his hand and Kissed him, then she followed into the kitchen where she had been preparing dinner.

Shepard's sixteen year old son, Kaiden casually came down the stairs hoping to find out what the family was having for dinner. Shepard hadn't told him that Bailey would be staying with them for the week. As he walked through the living room to enter the kitchen he saw a luggage bag laying across the couch. He figured it had been one of his father's friends, who frequently stayed at the house for various reasons.

When he turned the corner to the kitchen he was suprised by who was there. "Bailey!" He said enthusiasticaly as he hugged her.

Bailey couldn't help but smile, she didn't know that Shepard and Kelly hadn't told him she would be staying with them. "Hey Kaiden" then she leaned forward and kissed him.

The kiss would have lasted a lot longer but Kaiden remembered his parents were in the room also. "Umm... uhh- so why are you here?" He asked.

"Mom and Daddy wouldn't tell me" she answered. "They only told me said they were going somewhere and I'd have to stay here."

"Well, wanna go outside and talk?" He asked, hoping to get to talk to his girlfriend alone. She nodded and allowed him to lead her out the back door.

"So what have you been up to? I haven't seen you much lately."

Kaiden looked at her apologetically. "Sorry, I've been wanting to tell you, I've been going to the hospital a lot lately to get ready for my surgery." She looked scared, like she was afraid of losing him. "Don't worry, I'm not sick" her pale skin tone returned to its natural tan. "I'm going in to get my biotic implants two days from now." He finished.

"Are you going to be okay?" She asked as she embraced him again.

"Doctor Chakwas said it shouldn't be too dangerous, I'd like you to be there though when I get out." He requested.

"Of couse I will" she was about to kiss him but Kelly came up behindthem and told them to come in for dinner.

After dinner Kaiden helped Bailey makea make-shift bed out ofthe couch. "Too bad they won't let you sleep in my room with me" joked Kaiden as he passed her a thin quilt.

"In your dreams Kaiden" she smiled.

"What, I can't joke?"

"No, but I stillwanna pick on you" she said as she punched him softly and pulled him in for a kiss.

"Can we trust them to not try anything?" Asked Kelly as she and her husband slipped into bed.

"You don't have to worry about that, I installed a motion detector that will set of an alarm if either of them try anything." Grinned Shepard.

"Well, this is gonna be a long week isn't it... Kaiden told her about him getting his implants" she said changing the subject.

"Yea, he's gonna have to miss school, it takes a while to recover."

"He wants her to be there with him." She continued.

"I'll talk to the people at the school, I'll see what I can do, they can't call the Vega's they aren't able to comunicate with anyone until their mission is complete."

"You know something John." Investigated Kelly.

"I'm sorry, I can't exlain any of it, not even with you" he apologized as he cuddled closer to her. Soon both red headed adults were asleep.

_**Hey! I want more reviews this time, it keeps me motivated. **_


	2. Chapter 2

_**An: for all the people who notice I spelled Kaidan with an E. Its because its not Alanko its Shepard's son who is named after Kaidan.**_

It was late when Kelly, Bailey, and Kaiden got back to the house from the hospital. Kaiden was slumped in a wheelchair, still unconscious from all the meds that had been pumped into him during his surgery. Doctor Michel said that Kaiden would wake up if a few more hours. Kelly pushed her son up the metal stairs to his room and Bailey followed. When they got to his room they both lifted the sixteen year old into his bed.

"Can you stay up here with him while I call Shepard to see why the Council had to drag him away during Kaiden's surgery. They'd better have a good excuse." Sighed Kelly angrily. She felt as if the Council had begun over stepping their bounds more and more lately. Shepard had said he would be back soon but she hadn't received a call from him yet.

"Sure, Mrs. Shepard would it be okay if I slept in here tonight... just so I know he's fine?" Asked the fifteen year old girl.

Kelly stopped for a moment in the door way, nodded and said "but the door stays open at least." Bailey nodded happily and took Kaiden's sleeping bag out of the closet to lay on. "I'll be right back to scan his implant." Then Kelly walked out of the room after locking it open on its console.

Once Kelly was down stairs she went into her office and turned on her computer. It took a few minutes before Shepard answered, he looked tired. His shaven face had started to grow a stubble and he had light bags under his eyes, his short hair was just as disorganized as the Alliance dress blues he was wearing. "How's Kaiden?" Was the first thing out of his mouth.

"He's upstairs in bed, Bailey is watching him." Promised Kelly. "John, when will you be back?"

"Shouldn't be more than a day, they just wanted to alert me of something in person that they couldn't send over quantum entangler. We'll discuss it when I get back, we might need to bust out my equipment."

"Okay, hurry back please" she hoped, she sounded extremely concerned that her husband might need to shoot somebody again.

"Will do" then they each said their 'I love you's' and ended the call.

Kelly decided that she should probably grab something for Bailey and her to eat so she went into the kitchen and grabbed two sodas and a bowl of left over salad, along with two sets of smaller bowls and forks. She then proceeded to go upstairs and enter Kaiden's room.

She forked out half of the salad into one of the bowls and handed it to Bailey before sitting down at Kaiden's desk and doing the same for herself. "What's going on with the Council?" Asked Bailey after she took a bite of the salad.

"I don't know, I'm going to talk to Shepard about it when he gets home tomorrow. He couldn't tell me over the extranet." Said Kelly rolling her eyes. "Has Kaiden moved since we got home?"

"No, he's just laid there, how long do you think it will be before he's up and moving again?"

"Hopefully if a few hours" answered Kelly, "will you wake me up if he regains consciousness before morning?"

Bailey nodded and continued eating. They ate silently for a while, when Kelly was done Kelly got out the scanner that Dr. Michel had given her. She had Bailey hold the skin on the back of his neck tightly as she felt for the nerve bundle at the base of his neck. When she did, she stuck the needle at the end of it and watched the readings pass by on the screen. She was aware that his bio-electrical readings would be high for a while but it still made her worry about her son. "Okay Bailey, get some rest. I'm going to bed too because we weren't able to get you out of school tomorrow."

"Okay, I'll get you if he wakes up, night Mrs. Shepard." Said Bailey before she fell back into the sleeping bag and curled up. Then Kelly returned to Shepard and her's room.

**Can I please get some more reviews!**


	3. Chapter 3

Shepard was in his shuttle on the way back to Earth. The small shuttle was sparsely decorated, which reflected his dense military background. The citadel had been returned to its natural place in the nebulae, so Shepard had plenty of time to contemplate on what the Council and Specialist Traynor had told him.

_The Asari councilor was the only member of the council Shepard had saved - twice - that was still in that position. The Turrian's had assigned a new representative, she had golden face paint that went along the front of her nasal ridge and across her lower mandibles. Shepard could tell that the Salarian had also been part of the military, he wore his STG medals high on his tunic and always stood with authority. Shepard had met the human councilor before, at Admiral Anderson's memorial. She had short sandy colored hair and wore a white coat similar to the ones Shepard had seen captains wear in vintage Star Trek Shows during diplomatic missions._

_"Hello Commander" said the human councilor making her British accent extremely obvious. "We are sorry if we dragged you away from any of your obligations but this is something we couldn't simply allow to be said not in person - even over the most secure channels." _

_"What's going on Councilors?" Asked Shepard hoping to avoid the pleasantries. _

_"As you are know, Operative Ashley Vega and her husband Captain James Vega have been sent on a covert mission." Said the Turian Councilor as he leaned forward on the railing in front of him._

_"Yes, I read the briefing, did something go wrong with the mission?" Asked Shepard hoping that his two friends were still alive._

_The Salarian Councilor spoke this time. "To our knowledge the mission didn't get past their arrival at the relay. Our Intel hints that they had been boarded right as the Normandy exited the relay." The councilor entered something into his omni tool and a hologram of the Normandy appeared . "We have one person that was onboard when the Normandy was attacked that escaped." The Councilor motioned towards one of the doors on the empty balcony and a woman stepped out. Specialist Traynor stood on the balcony overlooking the meeting. "She managed to escape out of one of the escape pods." _

_Traynor had only slightly aged in the seventeen years since they had met. She looked like she was still twenty five but Shepard knew she was approaching forty. She was wearing an alliance jumpsuit and had her arm slung in a cast. "Hello Commander." Said the Specialist. The Council processed to allow her to tell a story of ho w the Normandy had been attacked when they started doing scans of the planet for pirate vessels before they approached the ocean planet. While they were doing that a Cerberus cruiser came out of the relay and disabled the Normandy. "I'm sorry commander, I couldn't do anything to stop them" she apologized. _

_"How do we know it was Cerberus? I thought all the cells were wiped out at the same time the Reapers were." Said Shepard._

_"That is what we had thought, but a week ago General Oleg was able to escape from an Alliance Prison ship. Along with the Traynor's testimony there is a lot of evidence that there is at least one cell left." Said the Human Councilor. "Two of our Spectre operatives have been sent to find the general and bring him in for questioning, but he is proving illusive." _

_"Okay, so my mission is to find the Normandy and bring back Ashley and James Vega?" Asked Shepard, he hoped Cerberus hadn't killed his friends yet. _

_"No Commander. We were making you aware of the situation, we will send a different Spectre to find the Normandy, Cerberus will be watching you too intently for you to be of any use." Ordered the Asari Councilor. "You are dismissed." Shepard nodded before leaving._

_Shepard was half way to his shuttle when Samantha caught him. "Commander!" She called as she came running up to him. Shepard stopped and turned around. "Shepard, may I accompany you back to earth, there is something I want to talk about in private and I need a ride to earth anyway."_

_"Okay, but what do you want to talk about?" Asked Shepard._

_"It's going to have to wait until we get to your shuttle" she said nervously._

Samantha Traynor entered the front compartment as they neared the relay. The sound of the door sliding shut woke Shepard from his dreams. "Thanks Commander for letting me use the back room to change out of that uniform." She was wearing a tight brown t-shirt and slim brown pants.

"No problem Traynor, but could you stop calling me commander. Call me John or at least Shepard" he said.

She took it as an order. "Okay, so what I wanted to tell you was that its not just Ashley and James that have been taken." Shepard looked at her strangely. "I was able to hack Ashley's data pad. Her true mission was to look into reports of Spectre's going missing."

"Why didn't you bring this up during the meeting!" Interrupted Shepard as they approached the relay.

"Do you know what would have happened to me if I had simply came up and said 'hello Councilors, I know why you sent Ashley to that system. It's because I hacked one of your top spectre's data pads!' I'd have been arrested or worst case scenario put on death row!" She blurt out. She looked scared, she respected both Shepard and Ashley and the Commander scared her more than a Krogan warlord. "I'm sorry Commander, my curiosity got the better of me" she apologized.

Shepard was about to continue scolding Traynor,but the com started beeping signaling a call coming threw. It was Kelly, she was probably wondering why he wasn't back yet and what had happened. "Go in the back compartment, we'll talk about this later." Shepard waited for her to leave before he answered. "How's Kaiden?" He asked before Kelly could talk.

"He's upstairs in bed, Bailey is watching him" promised his wife, he smiled. "John, when will you be back?" Asked Kelly.

"Shouldn't be more than a day, they just wanted to alert me of something in person that they couldn't say over quantum entangler. We'll discuss it when I get back, we might need to bust out my old equipment" he answered, his wife looked a little scared for what he might have to do.

She looked at him through the holographic screen for a moment and said nervously "Okay, hurry back." She made a kissy face to him.

"Will do" he promised. "Love you and see you soon."

"Love you too" she responded before ending the call.

_**An/ can I get some reviews, Some advice or recomendations would be great.**_


	4. Chapter 4

Bailey was half asleep when she heard a groan. She snapped to her feet and looked at her bed-ridden boyfriend. "Kaiden, how do you feel?" She placed her tan hand on his forehead softly.

Kaiden groaned. "Bailey?" His hand shakily moved to her other hand. "Where's my mom?"

"She'll be here in a second, how do you feel?" Bailey asked as she handed him a glass of water.

"Dizzy." He groaned as Bailey helped him sit up. He slowly brought the water up to his dry lips. He downed it quickly. "My head hurts."

"I'll be right back okay?" He nodded and Bailey kissed him on the cheek before departing to find Kelly. She came back with the mother close behind her.

"Hey Kaiden." Kelly spoke walking over to her only son. "I have to take your reading's, will you sit forward a little bit." Bailey had to help him stay steady, the drugs had yet to fully wear off. She held the small device over her son's neck. "This is gonna hurt, you ready?" Kaiden nodded slightly and Kelly slowly inserted the scanner's needle into the space between his spine and skull.

Kaiden tensed at the feeling of the cold needle entering his body. He held Bailey's hand tightly. His skin shimmered a slight blue as biotic static flared around his body. It took all his will to keep the static from flaring like lightning.

"Almost done Kaiden." Kelly comforted. "Just a little longer." She held her son's shoulder tightly so that the needle wouldn't hurt him. Kaiden moaned in pain, the scanner beeped two more times and Kelly eased the scanner out of his neck. "All done." She grinned. Kaiden fell back on his bed, the biotic static faded and eventually disappeared.

"Mom..." Kaiden's voice was still very dry. "Where is Dad?"

"He's on his way back, the Council had to speak to him in person." The door bell beeped a floor down. "That might be him now." Kelly spoke warmly as she hugged her son and walkd out the door.

Maya Brooks stood in the door way checking her equipment. She was wearing white Ajax armor, had her crusader shotgun in her hands and her tactical cloak was fully charged. Since she had rejoined the"new" Cerberus under General Oleg, she had felt more devoted to the cause - not that him breaking her out of the Alliance prison didn't help.

She had a squad of four trooper's standing behind her, all carrying harrier assault rifles. They had been deployed to surround the small house. Brooks' intel had told her that her target would be home when she and her squad arrived. The plan was for the target to open the door and once he did she would shoot the man, end of mission.

She pressed the "knock" button on the consol. She could hear somebody on the other side approaching. She aimed her gun right at where whoever it was would be standing,when the door slid open. When it did she unleashed a blast right into the figures chest, at that range even if they had shields they would have been utterly obliterated.

Blood sprayed in her face as the round pierced through the figure and imbedded in the wall on the other side of the room. "Crap..." She cursed as she realized it wasn't her target. She turned on her com and said "plan B, I repeat plan B." She could hear the sound of glass breaking as her men entered various parts of the house.

She headed straight for the upstairs bedroom. As she marched down the hall way she looked at pictures of the her target's family. She stopped at the last door. She could hear frantic searching on the other side of the door, probably _him _looking for a gun.

Maya Brooks blasted the door open using her gun's carnage modification. There stood Joel Pond, the owner of Kassa Fabrication. He had been a long time contributor to Cerberus up until the Illusive Man's death. After that he had given the Alliance the location of almost every remaining secret lad that had been left, now was his time to pay the price.

"Wait!" He pleaded. "I can give you money, is that what you want, credits?" He ducked behind his desk, hoping it would shield him from hr wrath.

"You son of a bitch." Cursed Brooks. "You don't even care that your wife is dead and you want me to let you live." She lowered her shotgun down to his head. "Too late to plead." She pulled the trigger and the house echoed with a loud _BANG!_

_**An/ hahaha, i got you, did you really think I'd kill Kelly. Anyway, sorry for taking so long. Well see you next month.**_


	5. Chapter 5

_**Sorry guys, really short chapter. Im gonna be really busy for the next month. I have a family trip that's honna be a few weeks, then i have band camp. Hopefully I can write somethimg durring that time**_

"Shep... John... will you do me a favor?" Samantha seemed extremely embarrassed. Shepard and her were in orbit above earth.

Shepard looked over at her slightly irritated. The woman had deceived the council and stole from their friend - even though her suspicions had proved correct - and here she was wanting him to help her. "What is it now Traynor?" His voice showed his irritation.

"I need a place to stay." She answered uncomfortably. "My girlfriend kind of kicked me out last month." She played with the pendant around her neck nervously. "Can I stay with you?... it'll just be a couple of days."

Shepard sighed. "Fine..." Shepard leaned back in his chair and covered his face tiredly. They were silent for a few minutes. "You think it would have been different if I had just killed the General on Omega? How am I supposed to tell Bailey her parents are missing?" He slammed his fists down on the controls. "When can I just move on from that damn war!"

Samantha didn't answer, she didn't have an answer. She felt sorry for her former Commander. She knew Shepard had been close with Ashley, they had been friends, but Traynor didn't know the whole story. "I... I don't really know. James talked about her a lot before the attack, I think she'll be able to take it." Traynor felt sorry for Shepard. "If I could have done anything to stop them, I would have."

"Thanks Sam." He gave her a fake smile and sat in silence the rest of the flight.


End file.
